Epigenetic mechanisms of adaptive plasticity in glioblastoma

About This Grant

Glioblastoma (GBM) is a highly malignant tumor of the brain that has a median survival of less than two years despite standard of care (SOC) therapy, which includes radiation (XRT) and temozolomide (TMZ). Targeting genetic mutations has not been successful in GBM due to the lack of ubiquitous genetic influences. Instead, GBM is more accurately defined as a disease of ‘cell states’ superimposed on a mutational background. These cell states are heterogeneous, and defined by non-genetic readouts such as transcriptome or epigenetic profiling, and are both highly dynamic and reversible (adaptive plasticity). Previous work has shown in in vitro models that resistance to targeted therapy can occur through epigenetic mechanisms that involve chromatin remodeling, a concept termed here as adaptive plasticity. The purpose of this work is to use mouse models, in particular glioma stem cell xenografts, to study single cell responses to treatment in vivo. The usage of xenograt models is part of all three Aims. In addition, profiling of SOC therapy response in complex models also demonstrated evidence of adaptive plasticity as a mechanism of tumor response to treatment. Therefore, cell state heterogeneity and adaptive plasticity are important mediators of GBM malignancy and resistance to therapy. Our LONG TERM GOAL is to translate information from single cell profiling methods into therapeutic strategies that target cell state heterogeneity and adaptive plasticity in GBM. Our OJBECTIVES FOR THIS PROPOSAL are to develop and validate methods for predicting cell state specific vulnerabilities based on epigenetic data, broadly characterize adaptive plasticity induced vulnerabilities during therapy using heterogeneous GBM tumor models, and validate targeting of chromatin remodeling mechanisms to circumvent adaptive plasticity. Our OVERALL HYPOTHESIS is that network based analysis of multiomic single cell data can inform strategies to overcome cell state heterogeneity and adaptive plasticity. Our SPECIFIC AIMS are: 1.) To test the hypothesis that we can predict cell state specific and adaptive plasticity induced vulnerabilities using network modeling approaches that incorporate multiomic epigenetic data (RNA-seq, chromatin profiling). To do this, we will leverage a large bank of glioma stem cell (GSC) lines to which we will apply multiomic profiling and make predictions regarding vulnerabilities based on network characteristics. We will test predictions by performing either CRISPR mediated knockouts or drug treatments targeting specific network vulnerabilities in a cell state specific context (both in vitro and in vivo). 2.) To test the hypothesis that repressive chromatin, particularly the remodeling of H3K27me3, is required for generation of cell state heterogeneity and adaptive plasticity, and that altering the dynamics of H3K27me3 could effectively prevent adaptive plasticity. We will accomplish this by testing knockout of H3K27me3 writers and erasers in GSC models both in vitro and in vivo at baseline and during targeted therapy. 3.) Identify additional epigenetic regulators of adaptive plasticity by performing a single cell screen targeting epigenetic modifying enzymes (~320) in the context of SOC. The knowledge gained from this proposal has the potential to identify cell state and adaptive plasticity informed strategies for improving outcomes in GBM patients.